Optical properties of adult Drosophila brains in one-, two-, and three-photon microscopy

mtFRC: depth-dependent resolution quantification of image features in 3D fluorescence microscopy

Motivation

Quantifying lateral resolution as a function of depth is important in the design of 3D microscopy experiments. However, for many specimens, resolution is non-uniform within the same optical plane because of factors such as tissue variability and differential light scattering. This precludes application of a simple resolution metric to the image as a whole. In such cases, it can be desirable to analyse resolution only within specific, well-defined features.

Results

An algorithm and software are presented to characterize resolution as a function of depth in features of arbitrary shape in 3D samples. The tool can be used to achieve an objective comparison between different preparation methods, imaging parameters, and optical systems. It can also inform the design of experiments requiring resolution of structures at a specific scale. The method is demonstrated by quantifying the improvement in resolution of two-photon microscopy over confocal in the central brain of Drosophila melanogaster. Measurement of image quality increases by tuning a single parameter, laser power, is also shown. An ImageJ plugin implementation is provided for ease of use via a simple Graphical User Interface, with outputs in table, graph, and colourmap formats.

Availability and implementation

Software and source code are available at https://www.imperial.ac.uk/rowlands-lab/resources/.

Three-photon excited fluorescence imaging in neuroscience: From principles to applications

The development of three-photon microscopy (3PM) has greatly expanded the capability of imaging deep within biological tissues, enabling neuroscientists to visualize the structure and activity of neuronal populations with greater depth than two-photon imaging. In this review, we outline the history and physical principles of 3PM technology. We cover the current techniques for improving the performance of 3PM. Furthermore, we summarize the imaging applications of 3PM for various brain regions and species. Finally, we discuss the future of 3PM applications for neuroscience.

Three-dimensional-generator U-net for dual-resonant scanning multiphoton microscopy image inpainting and denoising

A dual-resonant scanning multiphoton (DRSM) microscope incorporating a tunable acoustic gradient index of refraction lens and a resonant mirror is developed for rapid volumetric bioimaging. It is shown that the microscope achieves a volumetric imaging rate up to 31.25 volumes per second (vps) for a scanning volume of up to 200 × 200 × 100 µm³ with 256 × 256 × 128 voxels. However, the volumetric images have a severe negative signal-to-noise ratio (SNR) as a result of a large number of missing voxels for a large scanning volume and the presence of Lissajous patterning residuals. Thus, a modified three-dimensional (3D)-generator U-Net model trained using simulated microbead images is proposed and used to inpaint and denoise the images. The performance of the 3D U-Net model for bioimaging applications is enhanced by training the model with high-SNR in-vitro drosophila brain images captured using a conventional point scanning multiphoton microscope. The trained model shows the ability to produce clear in-vitro drosophila brain images at a rate of 31.25 vps with a SNR improvement of approximately 20 dB over the original images obtained by the DRSM microscope. The training convergence time of the modified U-Net model is just half that of a general 3D U-Net model. The model thus has significant potential for 3D in-vivo bioimaging transfer learning. Through the assistance of transfer learning, the model can be extended to the restoration of in-vivo drosophila brain images with a high image quality and a rapid training time.

Large-depth three-photon fluorescence microscopy imaging of cortical microvasculature on nonhuman primates with bright AIE probe In vivo

Multiphoton microscopy has been a powerful tool in brain research, three-photon fluorescence microscopy is increasingly becoming an emerging technique for neurological research of the cortex in depth. Nonhuman primates play important roles in the study of brain science because of their neural and vascular similarity to humans. However, there are few research results of three-photon fluorescence microscopy on the brain of nonhuman primates due to the lack of optimized imaging systems and excellent fluorescent probes. Here we introduced a bright aggregation-induced emission (AIE) probe with excellent three-photon fluorescence efficiency as well as facile synthesis process and we validated its biocompatibility in the macaque monkey. We achieved a large-depth vascular imaging of approximately 1 mm in the cerebral cortex of macaque monkey with our lab-modified three-photon fluorescence microscopy system and the AIE probe. Functional measurement of blood velocity in deep cortex capillaries was also performed. Furthermore, the comparison of cortical deep vascular structure parameters across species was presented on the monkey and mouse cortex. This work is the first in vivo three-photon fluorescence microscopic imaging research on the macaque monkey cortex reaching the imaging depth of ∼1 mm with the bright AIE probe. The results demonstrate the potential of three-photon microscopy as primate-compatible method for imaging fine vascular networks and will advance our understanding of vascular function in normal and disease in humans.

All-Optical Volumetric Physiology for Connectomics in Dense Neuronal Structures

All-optical physiology (AOP) manipulates and reports neuronal activities with light, allowing for interrogation of neuronal functional connections with high spatiotemporal resolution. However, contemporary high-speed AOP platforms are limited to single-depth or discrete multi-plane recordings that are not suitable for studying functional connections among densely packed small neurons, such as neurons in Drosophila brains. Here, we constructed a 3D AOP platform by incorporating single-photon point stimulation and two-photon high-speed volumetric recordings with a tunable acoustic gradient-index (TAG) lens. We demonstrated the platform effectiveness by studying the anterior visual pathway (AVP) of Drosophila. We achieved functional observation of spatiotemporal coding and the strengths of calcium-sensitive connections between anterior optic tubercle (AOTU) sub-compartments and >70 tightly assembled 2-μm bulb (BU) microglomeruli in 3D coordinates with a single trial. Our work aids the establishment of in vivo 3D functional connectomes in neuron-dense brain areas.

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All-optical volumetric physiology = precise stimulation + fast volumetric recording

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Precise single-photon point stimulation among genetically defined neurons

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3D two-photon imaging by an acoustic gradient-index lens for dense neural structures

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Observation of 3D functional connectivity in Drosophila anterior visual pathway

Millisecond two-photon optical ribbon imaging for small-animal functional connectome study

We developed a high-speed two-photon optical ribbon imaging system, which combines galvo-mirrors for an arbitrary curve scan on a lateral plane and a tunable acoustic gradient-index lens for a 100 kHz-1 MHz axial scan. The system provides micrometer/millisecond spatiotemporal resolutions, which enable continuous readout of functional dynamics from small and densely packed neurons in a living adult Drosophila brain. Compared to sparse sampling techniques, the ribbon imaging modality avoids motion artifacts. Combined with a Drosophila anatomical connectome database, which is the most complete among all model animals, this technique paves the way toward establishing whole-brain functional connectome.